Links

• Plant Sciences is the third best degree subject for graduate starting salary (after medicine and dentistry). Woop woop!

• The genome of bread wheat has been sequenced. Not only is this an impressive feat (the wheat genome is a very large and complicated thing which arose through the fusion of three other genomes) it is also very promising in terms of feeding the world. About 20% of human calories come from wheat, and knowing the genome will make it easier to improve the crop in the future. 

• I've decided to start a new feature called 'Article Title of The Month'. I'm pleased to announce that the winner for November 2012 is 'Sex in Cheese: Evidence for Sexuality in the Fungus Penicillium roqueforti'. 

• I'm really struggling to find more broccoli-based entertainment. Let me know if you are aware of anything good. 

"We Must Remove the Landmines That Limit Access to Biotechnology in Africa" - Motlatsi Musi

An interesting article about the potential benefits of GM in Africa:

"GM technology is not a panacea. It won’t solve all of our problems. African farmers face a long series of challenges, from an inadequate infrastructure to political corruption. Yet access to the latest crop technologies will give us a fighting chance, especially as the climate changes and we try to adapt to new and possibly harder conditions. Drought-resistant plants represent an especially hopeful opportunity.

Too much of Africa missed out on the Green Revolution. We cannot afford to let Africa ignore the Gene Revolution. Unfortunately, many people, especially in Europe, don’t want us to benefit from these developments..."

Read the full article here: http://www.truthabouttrade.org/2012/11/21/we-must-remove-the-landmines-that-limit-access-to-biotechnology-in-africa/

Hat tip: GMO Pundit 

Genetically Modified Apples That Don't Brown!

Read all about it here: http://www.biofortified.org/2012/07/okanagan-specialty-fruits/

Here is a jack-o'-lantern made from one of the apples. Note how white the flesh is.

Picture from http://www.biofortified.org/2012/11/contest-winner-ghoulish/

Links

• One of the oldest, and most controversial, groups of GM crops are the so-called 'herbicide-tolerant' crops. These crops have been engineered to be resistant to certain chemical herbicides, so these herbicides can be sprayed to kill weeds without having to worry about having any affects on the crop. There is a lot of debate about them, and I'm not really sure where I stand on it. Anyway, this PDF from Purdue University explains some of the basic facts. 

• This brilliant article explains that Italian scientists, who failed to predict an earthquake that was impossible to predict, should not have been sued for manslaughter. 

• The genome of a pear has been sequenced. The exciting thing is that we live in an age of such advanced sequencing technology that this isn't really big news. 

• One of the most promising avenues for developing new biofuels is to break down cellulose (the material that plant cell walls are made of) to form sugars that can be fermented to make fuel. This would allow us to convert inedible parts of crops, such as the stems of corn plants, into fuel. Scientists are constantly looking for better ways of breaking the cellulose down, and this report suggests that we may be able to get algae to do it for us. 

• More exciting biofuels news. 

• A fantastic paper about some really common problems with the way that statistics are reported in scientific research. Anyone who plans on writing a scientific paper about any kind of research should read this.  

• ATTACK OF THE KILLER BROCCOLI!!!!

Is Resistance Futile? How useful can GM really be in the battle to protect our crops?

Anyone who has studied military history will probably be familiar with the concept of an 'arms race'. One army develops some new type of weaponry which gives them the edge over their rival. The rival responds by developing a slightly better type of weaponry so that they now have a slight edge. This prompts a new development from the first army, which then prompts another new development from the second, and so on. As the process continues, both armies make a great deal of progress in terms of military technology, but very little progress in terms of their ability to overpower the other rival. They are both always either slightly stronger than, slightly weaker than or roughly the same strength as the other army.

Arms races are not just a human phenomenon, but are also a key part of evolution, including plant evolution. All plants are constantly locked into evolutionary arms races with two groups of living things: pathogens (organisms such as microbes and viruses that cause disease) and pests (organisms such as insects and grazing mammals that eat plants). As soon as a plant species evolves a new line of defence (a new poison perhaps), these pathogens and pests begin evolving some way of overcoming that defence (an antidote, for example). This arms race occurs not because the organisms want to outdo each other, but because of the inevitable pull of natural selection.

A cabbage plant which happens (not through design, but through sheer genetic luck) to be born with a new type of anti-slug poison will be more successful than the other cabbages around it and will produce more seed. Its offspring (which inherit the new line of defence) will similarly out-compete the cabbages around them. Within a few generations, the entire field will be full of slug-proof cabbages. It is only a matter of time, however, before a slug is born which (not through design, but through sheer genetic luck) is resistant to the poison. This fortunate creature will have access to all of the cabbage that the other slugs cannot eat and will therefore grow big and strong and produce lots of babies. Before long, all of the slugs in the field will be resistant to the poison. And so the arms race goes on. It is important to note the this slug only had an advantage because the poison existed. If the the poison did not exist then this slug would have had an antidote to a non-existent poison, which is no advantage. The existence of a defence actually causes the evolution of a counter-defence. It is a battle that has been raging for hundreds of millions of years and is not going to stop any time soon.

At some point, just a few thousand years ago, we got ourselves involved in this fight, and ever since we have been doing everything we can to protect our crops from pests and disease. Our most recent weapon is the use of genetic modification to give crops defence mechanisms that they might never have evolved naturally. For example, there are a group of genetically modified (GM) crops called the 'Bt crops' which have been given genes from a bacterium in order to protect them from insects that like to eat them.

The bacterium which donated the genes is a soil-dweller called Bacillus thuringiensis (Bt for short). Bt has a set of genes that allow it to produce a special group of anti-insect proteins. If an insect eat the bacterium, these proteins damage the inside of that insect's stomach, causing it to die. For decades, farmers (including organic farmers) have sprayed the bacterium onto their crops as a form of natural pesticide. Each of the anti-insect proteins affects only one type of insect, meaning that there is no harm to other organisms in the field, or to humans who eat the food.

There are two drawbacks to spraying crops with the bacterium. Firstly, it can be washed off by rain. Secondly it does not get inside plant stems, which is where some insects (such as the corn borer) like to lay their young. Transferring the Bt genes to crops solves these problems because it means that the plants themselves produce the proteins.

In the late 90s Bt cotton and Bt corn (which each contain one Bt gene for one Bt protein) were invented. They are now grown on hundreds of millions of acres around the world (mostly in the USA, Australia, China and India, but they are becoming more widespread in other countries; other Bt crops such as Bt rice are also in the pipeline). Not only has this raised yields, it has also reduced the use of pesticides, which can be harmful to the environment due to, among other things, their effects on non-target insects. In many countries, such as India and China, farmers previously sprayed powerful pesticides from containers on their backs, resulting in many farmers being poisoned. Since the introduction of Bt cotton the number of poisonings has gone down significantly.

But there is a problem with Bt crops, which you might be able to guess by now. At some point an insect might be born which is resistant to one of the Bt proteins. This would give it an advantage and before long there would be many resistant insects. Unfortunately, this has already happened, multiple times in multiple countries (including the USA, Pakistan and China). At the moment, resistant insects account for only few percent of the insect pests in those areas, but if nothing is done, it is only a matter of time before Bt-resistance spreads and Bt-crops become completely useless. But what can be done?

Well, ever since Bt crops were first grown, scientists have tried to prevent insects from becoming resistant by urging farmers to plant 'refuges' of non-Bt crops next to their Bt crops. This reduces the advantage that a Bt-resistant insect would have, since the other insects can still find some food. However, the advantage is only reduced, not completely eliminated, so while this strategy can delay the problem it cannot completely prevent it.

So is it hopeless to expect GM to protect our crops in a sustainable way? Well, actually, it might not be.There is a new technique called 'engineering durable resistance' that might just put an end to the arms race. It is a very simple idea and it works like this: rather than giving a GM crop one way to kill a pest or pathogen, you give give it multiple ways to kill that one pest or pathogen. For example, a new version of Bt cotton has been released in the US and Australia, which has two different Bt proteins that both kill the cotton bollworm. Now, a cotton bollworm which is born with resistance to one of the proteins has absolutely no advantage, because the cotton plant will still kill it. In order to have an advantage a bollworm would have to be born with resistance to both proteins, which is very unlikely. If the number of proteins was increased to say, 4 or 5, then the chances of a bollworm being born with resistance to all of them are vanishingly small.

Of course, it is impossible to know for certain whether this represents a long-term victory. In theory, durable resistance should provide lasting protection, but theory doesn't always turn out to be right. The appropriate response at this stage is probably something along the lines of quiet optimism.

I just discovered these 3 short videos about genetic modification...

...and I think they're quite good.

News from the journals

A few interesting stories from recent papers published in scientific journals:

Soybeans adapt to Chernobyl's radioactive soil by improving their heavy metal tolerance

The disaster that occurred at Ukraine's Chernobyl Nuclear Power Plant in 1986 was probably the worst nuclear accident that there has ever been. But despite the devastating size of the disaster, plant life continues to grow in the radiation-contaminated area. In order to investigate how plants manage this surprising survival trick, a team of scientists from Ukraine and Slovakia planted soybean seeds in two fields in the Chernobyl area in 2007. The two fields were very similar in terms of soil type, but one of them was radioactive and the other one wasn't. A year later the scientists harvested and analysed the soybeans. They found that after a year's exposure to radiation the plants in the radioactive field were different, in a number of interesting ways, from the plants in the non-radioactive field. Notably, they had adapted to be more tolerant of the heavy metals that cause the nuclear contamination.

Like most scientists who do something cool because of curiosity, but need to find practical reasons to justify the funding they receive, the researchers end their recent paper by suggesting ways that further experiments into this subject could be useful. Their first suggestion is that with a better understanding of how plants adapt to the radioactive environment, it could be possible develop ways of growing biofuel crops in the area (which, for obvious reasons, is not currently used for growing food crops). If you think that this represents some serious out-of-the-box thinking, then wait until you see their second suggestion:

"With a little of imagination, it is also tempting to speculate that understanding plant adaptation toward ionizing radiation (cosmic radiation) will be necessary for plant cultivation for food purposes during long space missions in the future."

[Read this paper for yourself at: dx.doi.org/10.1371/journal.pone.0048169]


Using a computer model to test ideas about plant cell wall structure

Just like animals, all plants are made up of little bags of life called cells. In plants (but not in animals) each cell is surrounded by a rigid structure called the 'cell wall'. Cell walls give plants shape, strength and stability (qualities we achieve with our muscles and bones).

Although we know what components plant cell walls are made from, we still only have educated guesses about how these components are arranged. One of the most popular ideas is that strong tubes called 'cellulose microfibrils' (they are a bit like tiny scaffolding poles) are held together by long, stringy molecules called 'hemicelluloses', in an arrangement something like that shown in the diagram below. The theory is that this binding together of the cellulose microfibrils is what gives the cell wall its large amount of strength.

In order to test this idea, two researchers from Pennsylvania State University have created a computer simulation of a cell wall, complete with simulated cellulose microfibrils and simulated hemicelluloses to hold them together. Once the simulation had been produced, they asked the computer what would happen if the cell wall was stretched, and whether the result would be different if the links between the two components were removed.

They found that the presence of the links does make a big difference. Without them, the simulated cell wall was much less able to withstand stretching. This is an important piece of evidence which suggests that this arrangement may actually be how the components are arranged in real life. However, they also found that even with the links, the cell wall was still not strong enough to withstand certain types of stretching that real-life cell walls could easily cope with. This suggests that in real-life, cell walls must have other, additional mechanisms to resist stretching.

[Read this paper for yourself at: dx.doi.org/10.1104/pp.112.201228]



Genetically Modified Soybeans with increased beta-carotene content

A few weeks ago I wrote about Golden Rice, a variety of rice which has been genetically modified to produce beta-carotene (an important, but often absent, component of human nutrition). Now, a team of Korean researchers have genetically modified Soybean to do the same thing.

[Read this paper for yourself at: dx.doi.org/10.1371/journal.pone.0048287]

The Pervert's Guide To Plants

Are you a deviant who likes to hear saucy stories? Have you grown tired of the tame tales that your fellow humans have to tell you? If so, then step right this way. The mind-blowing wonders of a plant's sex life are far, far weirder than anything you will find in Fifty Shades of Grey. 

For starters, in the plant world there is sperm flying all over the place - literally! Pollen cells are a plant's sperm cells (I don't mean metaphorically, they are actually called 'sperm cells'). Just like human sperm cells they are produced in the male sexual organs, contain half the amount of genetic material (DNA) required to produce a new individual, and fertilise egg cells to produce embryos.

Pollen grains (shown here) contain sperm cells. A fact which puts hay-fever in a whole new light. 

Unlike human sperm, pollen isn't usually transferred by direct contact between a male and a female. Instead it is carried on the wind or by unwitting insects, birds and small mammals who are drawn in by the beauty of flowers and the promise of sweet nectar. The animal gets dusted with pollen while visiting one flower and then unknowingly carries it to the next flower that it visits, where it deposits some of the pollen onto the egg cells, resulting in fertilisation. Plants, in other words, use wild animals to carry their sperm into the female sex organs of other plants. The bee orchid, perhaps the most ingeniously perverse and sexually manipulative of all plants, has evolved to look like a female bee so that horny male bees will fly over and hump it. In doing so, the bee gets covered in sticky pollen which it then unintentionally carries to the next orchid and deposits on the eggs. (Incidentally, humans also seem to find orchids sexual: the word 'orchid' itself comes from the Greek word for 'testicle'. Apparently the roots look like balls. I'm not convinced.)

To a male bee, this is preeeeety sexy.

Given that they rely on the wind and hungry (and sometimes horny) animals as couriers for their sperm, it is not surprising that plants are never monogamous: they usually have sex with many different partners. Often a single male will fertilise many females at the same time (a practice which does occur in human societies, but is generally frowned upon). But it is not just the males who tend to be highly promiscuous - a single female can be fertilised by the pollen of many different males and carry the embryos of all of their offspring (inside seeds) at the same time. (I was fairly sure this never happened in humans, but according to these internet randomers, it occasionally does...).

The distinction between male plants and female plants is often not a valid one. In many plant species every plant has both male and female sexual organs. In other words, the plant kingdom has a lot of hermaphrodites. Usually the male sexual organs (stamens) are located around the female ones (ovaries). Given the temptingly close positioning of the pollen (orange circles in the image below) and the eggs (green blobs labelled 'ovule') you might wonder if plants are ever caught having sex with themselves. The answer is an enormous yes. Self-pollination is rife, and they don't just do it for fun, it is a common mode of reproduction. Domesticated wheat plants, for example, tend to release all of their pollen before the flower opens, meaning that none of it escapes. It all stays within the flower resulting in self-fertilisation.

Phwoar

So there you have it, plants are promiscuous, manipulative and just plain weird. If that's not enough for you, then I suggest you check out what the fungi have to offer. Oh, and remember to delete your internet history.

More Links

A sexy new blog post is on its way. In the meantime, I will compensate for my laziness with links to things that other people wrote/made:

• The most exciting interactive 3D render of broccoli you will ever see!
• As my grandma always said, 'if it works for science undergraduate students, then it'll work for blueberry growers in Maine'. 
• An interesting opinion article on the current debate in the US surround labeling of GM foods. 
• Another one!
• Last summer, I spent some time working in the new laboratory at Cambridge University's botanic gardens. I helped to stack the shelves of its library and install wooden draws in its herbarium. Now it has won a prestigious architecture prize. Not that I'm claiming credit or anything...

Golden Rice: A GM crop designed to fight malnutrition

It is well known that there a lot of people in the world today who are malnourished. Unfortunately, this problem is actually two problems. The first is that people do not have enough food to eat. The second is that people don't have access to the right type of food. One of the most serious examples of this second problem is vitamin A deficiency. This post is the story of Golden Rice, a genetically modified (GM) crop designed to help prevent vitamin A deficiency. 

Vitamin A is an essential part of a healthy diet. Not having enough of it leads to night blindness, anemia, and a weakened immune system, with particularly bad effects in children and pregnant women. The effects on the immune system are particularly troubling since most of the countries that suffer from vitamin A deficiency also have high rates of infectious diseases. Vitamin A deficiency weakens a person's immune system leaving them vulnerable to these diseases. Infection with disease often then leads to a reduced appetite and reduced absorption of any vitamin A that is consumed, meaning that the person becomes even more vitamin A deficient, which in turn makes them even more vulnerable to disease. It is a vicious cycle.

The easiest way to get enough vitamin A is to eat animal products, but if the human body doesn't get enough from that source then it can also make its own vitamin A from another chemical, called beta-carotene. Beta-carotene is an orange-coloured pigment found in many fruits and vegetables - for example, it gives carrots their orange colour. When you eat fruit and veg that contains beta-carotene your body turns that beta-carotene into vitamin A. Unfortunately, there are many people in the world, especially in Africa and South Asia, who do not get enough vitamin A because their diet is not high in meat or vegetables. Instead, their diets are mainly based around rice, and while the rice plant itself does produce beta-carotene, it does so only in the leaves and stem. No beta-carotene is found in the grain (the part that people eat). This means that vitamin A deficiency is a big problem in these regions. Approximately one third of the world's preschool-age children are estimated to be vitamin A deficient and when only Africa and South-East Asia are considered, this figure rises to approximately 44-50%. It has been estimated that making enough vitamin A available to all of the world's children would prevent around 2 million child deaths per year.

This is where Golden Rice comes in. Golden Rice is a variety of rice that has been genetically modified to make it produce beta-carotene in the grain. Since beta-carotene is an orange pigment, this means that the rice grains are orange instead of white (as shown on the left in the picture below), which is where the name 'Golden Rice' comes from (okay, so orange and gold aren't quite the same colour, but I guess 'orange rice' would have sounded a bit rubbish).

Golden Rice grains (left) and normal rice grains (right)

At the moment, Golden Rice is still going through the regulatory process that all new GM crops have to go through. Once it is ready to be used, the seeds will be given to poor farmers around the world for free. It has been bred with local varieties in the regions that it is being given to, so that it has the same characteristics as the rice that people are used to. Farmers won't have to change their growing practices and consumers won't have to change their cooking habits. The only difference will be that they will be getting a healthy dose of beta-carotene with each bowl of rice they eat. Just like normal rice, farmers will be able to reuse the seed from one harvest in order to grow rice for the next season. This means that the new seeds only have to be distributed to each region once. 

Although Golden Rice has not yet been given to any farmers, the project has been underway for at least twenty years. Scientists began working on it in 1992 and it was in 1999 that they first managed to produce rice that made beta-carotene in its grains. However, the levels of beta-carotene produced were considered too low. Although this rice would have provided more beta-carotene than normal rice, it did not have high enough levels to completely fulfill the needs of people who are eating little else than rice. The experiments continued and by 2005 the scientists had managed to get the beta-carotene up to a much higher level. It has been shown that about 100-150g of this new version of Golden Rice can provide about 60% of a child's daily vitamin A requirement. Since then, the rice has been going through various tests to prove that it is safe for people to eat and that it won't harm the environment. The people behind the project are currently working with regulators in some target countries and hope to transfer Golden Rice seed to some farmers in the next few years. 

Many of the people who work on the Golden Rice project feel that progress so far has been unnecessarily slowed down by excessive regulation of GM crops. One the plant's two co-inventors, Ingo Potrykus, wrote an article in the scientific journal Nature in which he argued that there is no logical reason for new GM crops to have to undergo any more tests than other types of new crop. He argues that the the current regulations on GM crops are putting unnecessary financial and time constraints on the development of crops that could otherwise be preventing death and suffering. 

There are others, however, who think that Golden Rice seeds should never be given to any farmers at all. For example Greenpeace, who are opposed to all GM crops, have written articles criticizing the Golden Rice project (for example, this one and this one). Not only do they think that the new rice is a dangerous, untested technology, they also feel that it is completely unnecessary given the other strategies that are available to combat vitamin A deficiency. 

In general, I tend to agree with the scientists from the Golden Rice project on these issues. However, a full discussion of my reasons for this would take a few more posts, and it is certainly something that I plant to write about in the future. For now though, I just wanted to present the basics of the story. Anyone who wants to read more about the Golden Rice project, or the science that enabled it should take a look at www.goldenrice.org and anyone who wants to read some of the arguments being made against it should have a look at some of these articles: 

http://www.greenpeace.org.uk/search/node/golden%20rice. 

Some Links

• The most exciting footage of broccoli you will ever see.

• Using medical scanners to prove that there's nothing special about the wood in antique violins. Hopefully there weren't patients waiting to be scanned when they did this. For context, see also this blind test.  

• Carl Zimmer, last month, warning against a "rancid, corrupt way to report about science".

• Hooray for cheap booze!

• Two unashamedly nerdy plant scientists talk about genetic modification, among other things. 

A new challenger for title of 'world's coolest plant'?

Carnivorous plants (plants that eat animals) are very important to a plant science fan like me. This is because they are the only plants which are universally regarded as cool. Of course, I think that all plants are totally super wicked awesome, but that is generally not something that I choose to say out loud in front of other humans. Carnivorous plants give me an opportunity to talk about plants in public places, without concealing my identity, and yet not give away just how much of a massive plant-nerd I am. If I was trying to get all of my favorite plants into a trendy nightclub, I would send the carnivorous plants first. They would have no trouble getting in. Then if the daisies and sunflowers got stopped because they 'didn't meet the dress-code' or 'weren't on the list', the carnivorous plants could turn around and say, "it's cool man, they're with us".

 By far the most famous of the carnivorous plants is the Venus Flytrap. There is a good reason for this: it's truly bad-ass, as David Attenborough will tell you (well, okay, he doesn't use those exact words). With it's touch-triggered jaws of eternal doom, the Venus Flytrap is the uncontested coolest of the cool. Or is it?

 A few weeks ago, a group of six German-based scientists published a paper in which they promote another contender for the title of coolest kid in the plant kingdom: the Pimpernel Sundew. Much like the Venus Flytrap, this sundew doesn't just have a bad-ass name, it also has a bad-ass way of catching its prey. Like all sundews, it has special leaves covered in drops of glue, which trap and suffocate insects allowing the plant to digest them, but that's not the exciting bit. The Pimpernel Sundew takes things up a notch in a way that hasn't been observed in any other plant species. Surrounding the sticky leaves, it has a ring of 'snap-tentacles' that act as catapults. Every time an unsuspecting insects lands one of these mini-catapults, the tentacle snaps quickly and flings the helpless animal onto the inner leaves where it meets its gluey fate. If you can can't imagine just how awesome this heartless insect-munching machine is, then I suggest you watch this video, which the researchers included with their paper:

 Although they don't quite come out and say it in their paper, the researchers clearly think that the Pimpernel Sundew deserves at least as much street-cred as the Venus Flytrap. In their introduction, they make a point of mentioning that the catapults "can bend within a fraction of a second, similar to the speeds reported for the Venus Flytrap". This is scientist-speak for "mine's just as quick as yours". They also clearly think that public recognition for the coolness of this catapult of insect death is long-overdue. They note that although the fly-flinging mechanism was first discovered in 1974, "remarkably, these fascinating observations and interpretation received no consideration until 2010, and trapping action in D. glanduligera has not been documented or investigated in depth until now."

 Although they did do some actual experiments and did manage to work out a biological mechanism by which the catapults are able to snap so quickly, I think the real reason for publishing this paper is clear. The authors are obviously fed-up with the Venus Flytrap stealing the limelight. They think that the Pimpernel Sundew is way more cool, and they've decided that it's time to tell the world. 

 This is an exciting time to be a carnivorous plant. The Venus Flytrap's long reign as undisputed champion of cool is being threatened and we may soon have a new world's coolest plant. At the very least, there will be a bit more room for debate. My guess is that, just like Superman vs. Batman, Ketchup vs. Brown Sauce and Lenny vs. Carl, this battle is one that will rage on forever. 

[NOTE: Because the paper was published in the open-access journal PLoS ONE (woo!), you can read the whole thing for free at:  http://dx.doi.org/10.1371/journal.pone.0045735]